Pelagophyceae

RCC

Metabarcodes

Datasets included

All public data sets
dataset_id dataset_code dataset_name gene_region
1 OSD_2014_V4_LGC Ocean Sampling Day - 2014 - V4 LGC V4
2 OSD_2015_V4 Ocean Sampling Day - 2015 - V4 V4
3 OSD_2014_V4_LW Ocean Sampling Day - 2014 - V4 LW V4
5 MALINA_Monier_2014 Arctic Ocean, Beaufort Sea, MALINA cruise - 2009 V4
6 Arctic_Stecher_2016 Central Arctic Ocean - 2012 V4
9 Nansen_Metfies_2016 Nansen Basin - 2012 V4
11 Fieldes_Bay_Luo_2016 Fieldes Bay, Antarctic - 2013 V4
19 Baltic_Sea_2012_2013 Gulf of Finland - 2012-2013 V4
20 Oslo_fjord_2009_2011 Oslo fjord - 2009-2011 V4
33 Tsunami_18S Tsunami deposits 18S R1 V4
34 Malaspina_vertical_V4 Malaspina expedition - vertical profiles - 2010-2011 V4
35 Malaspina_surface_V4 Malaspina expedition - surface - 2010-2011 V4
36 Blanes_2004_2013 Blanes Time Series - 2004-2013 V4
37 Baffin_Bay_Joli_2013 Baffin Bay - 2013 V4
38 White_Sea_2013_2015 White Sea - 2013-2015 V4
39 Arctic_Ocean_PS80_2012 Arctic Ocean - Polarstern expedition ARK-XXVII/3 - 2012 V4
40 Arctic_Ocean_Survey Arctic Ocean Survey - 2005-2011 V4
41 Chukchi_Sea_ICESCAPE Chukchi Sea - ICESCAPE - 2010 V4
42 Arctic_Nares_Strait Nares Strait - 2014 V4
43 Baltic_Gdansk_2012 Gdansk Gulf - 2012 V4
44 Baltic_Gdansk_2012_Hapto Gdansk Gulf - 2012 Hapto V4
49 Naples_2011 Bay of Naples - 2011 V4
53 Biomarks Biomarks V4
15 Tara_Oceans Tara Oceans - 2009-2012 V9
Data sets selected
dataset_id dataset_code dataset_name gene_region
1 OSD_2014_V4_LGC Ocean Sampling Day - 2014 - V4 LGC V4
2 OSD_2015_V4 Ocean Sampling Day - 2015 - V4 V4
34 Malaspina_vertical_V4 Malaspina expedition - vertical profiles - 2010-2011 V4
35 Malaspina_surface_V4 Malaspina expedition - surface - 2010-2011 V4
36 Blanes_2004_2013 Blanes Time Series - 2004-2013 V4
53 Biomarks Biomarks V4
15 Tara_Oceans Tara Oceans - 2009-2012 V9

Summarize functions

Maps

map_asv_set <- function(one_asv_set, directory) {
  
# one_asv_set <- filter(asv_set[["V4"]]$df, dataset_id != 36)
# directory = "../metabarcodes/V4/"
  
  world <- map_data("world")

  # g <- ggplot() + 
  #   geom_polygon(data = world, aes(x=long, y = lat, group = group), fill="grey") + 
  #   coord_fixed(1.3) +
  #   geom_point(data=one_asv_set, aes(x=longitude, y=latitude, size=pct_class), fill="blue", shape=21) + 
  #   # scale_size_area(trans="log10") +
  #   ggtitle("Percent of Pelagophyceae") +
  #   facet_wrap(vars(species))
  # print(g)

  df <- one_asv_set  %>% 
    select(longitude, latitude, pct_pelago_total) %>% 
    rename(z=pct_pelago_total) %>% 
    distinct()
  gg <- map_distribution(df, 
                         map_title = "Pelagophyceae - % of Total reads",
                         z_limits = c(0, 10),
                         z_breaks = 1*c(1, 2, 4, 6, 8, 10),
                         z_min = 0.01)
  print(gg)
  ggsave(plot= gg , filename=str_c(directory,"map_Pelago_pct_total.pdf"),
     width = 15 , height = 12, scale=1.80, 
     units="cm", useDingbats=FALSE)  
  

  for (one_species in unique(one_asv_set$species)) {
    df <- one_asv_set %>% 
      filter(species == one_species) %>% 
      select(longitude, latitude, pct_class) %>% 
      rename(z=pct_class)
    
    gg <- map_distribution(df, 
                           map_title = str_c(one_species," - % of Pelagophyceae"),
                           z_min = 0.01)
    print(gg)
    ggsave(plot= gg , filename=str_c(directory,"maps_pct_pelago/map_",one_species,"_pct_pelago.pdf"),
       width = 15 , height = 12, scale=1.80, 
       units="cm", useDingbats=FALSE)
  }
  
  # for (one_species in unique(one_asv_set$species)) {
  #   df <- one_asv_set %>% 
  #     filter(species == one_species) %>% 
  #     select(longitude, latitude, pct_total) %>% 
  #     rename(z=pct_total)
  #   gg <- map_distribution(df, map_title = str_c(one_species," - % of Total reads"),
  #                          z_limits = c(0, 1),
  #                          z_breaks = 0.1*c(1, 2, 4, 6, 8, 10))
  #   print(gg)
  #   ggsave(plot= gg , filename=str_c(directory,"maps_pct_total/map_",one_species,"_pct_total.pdf"),
  #      width = 15 , height = 12, scale=1.80, 
  #      units="cm", useDingbats=FALSE)
  # }


  return(TRUE)
   
    
  }

Summarise the data

  • Maps are only for surface samples

V4 - OSD 2014-2015, Malaspina, Blanes, Biomarks

[[1]]


genus                      species                         n_reads    pct_class   pct_total
-------------------------  -----------------------------  --------  -----------  ----------
Ankylochrysis              Ankylochrysis_lutea                1124    0.3534281   0.0016651
Ankylochrysis              Ankylochrysis_sp.                   115    0.4789488   0.0002084
Aureococcus                Aureococcus_anophagefferens       32697    7.9762765   0.0310217
Aureoumbra                 Aureoumbra_lagunensis                50    0.1202055   0.0001139
Chrysocystis               Chrysocystis_fragilis              2799    1.4307706   0.0020358
Chrysoreinhardia           Chrysoreinhardia_sp.                  2    0.0000070   0.0000020
Pelagococcus               Pelagococcus_sp.                   6110    3.4071300   0.0075800
Pelagococcus               Pelagococcus_subviridis               1    0.0003316   0.0000011
Pelagomonadaceae_clade_A   Pelagomonadaceae_clade_A_sp.      23710    9.2576480   0.0249426
Pelagomonadaceae_X         Pelagomonadaceae_X_sp.              351    0.1036844   0.0005932
Pelagomonas                Pelagomonas_calceolata           720265   40.5003490   0.6885337
Pelagophyceae_Svalbard     Pelagophyceae_Svalbard_sp.          498    0.2980440   0.0011230
Pelagophyceae_XXX          Pelagophyceae_XXX_sp.             50968   11.2727535   0.0481332
Pulvinaria                 Pulvinaria_sp.                        4    0.0001133   0.0000009
Sarcinochrysidaceae_X      Sarcinochrysidaceae_X_sp.           800    1.5698927   0.0015097
Sarcinochrysis             Sarcinochrysis_sp.                12502    7.6793874   0.0171452

[[2]]


substrate       n
----------  -----
sediment       24
water        1000

[[3]]


depth_level       n
-------------  ----
anoxic            7
bathypelagic     63
bottom           24
DCM              45
euphotic         37
mesopelagic      60
surface         788

[[4]]


fraction_label      n
---------------  ----
NA_     NA         24
0.00_   0.20        9
0.20_   3.00      120
0.22_     NA      293
0.22_   3.00      303
0.80_   3.00       38
3.00_  20.00      205
20.00_2000.00      32

[1] TRUE

[1] TRUE

V9 - Tara Oceans

[[1]]
# A tibble: 6 x 5
# Groups:   genus [6]
  genus                   species                    n_reads pct_class pct_total
  <chr>                   <chr>                        <dbl>     <dbl>     <dbl>
1 Aureococcus             Aureococcus_anophageffere~  887561    16.6   0.0800   
2 Pelagococcus            Pelagococcus_sp.             25784     3.67  0.00374  
3 Pelagomonadaceae_clade~ Pelagomonadaceae_clade_A_~   16250     4.24  0.00157  
4 Pelagomonadaceae_X      Pelagomonadaceae_X_sp.       18632     2.77  0.00158  
5 Pelagomonas             Pelagomonas_calceolata     3210461    70.9   0.311    
6 Sarcinochrysidaceae_X   Sarcinochrysidaceae_X_sp.      473     0.222 0.0000379

[[2]]
# A tibble: 1 x 2
  substrate     n
  <chr>     <int>
1 water       884

[[3]]
# A tibble: 3 x 2
  depth_level     n
  <chr>       <int>
1 euphotic      306
2 mesopelagic    70
3 surface       508

[[4]]
# A tibble: 12 x 2
   fraction_label       n
   <chr>            <int>
 1 "  0.22_   3.00"     1
 2 "  0.80_     NA"   112
 3 "  0.80_   3.00"    29
 4 "  0.80_   5.00"   175
 5 "  0.80_  20.00"     8
 6 "  0.80_ 200.00"     2
 7 "  3.00_     NA"    35
 8 "  3.00_  20.00"     1
 9 "  5.00_  20.00"   165
10 " 20.00_ 180.00"   168
11 " 20.00_ 200.00"     8
12 "180.00_2000.00"   180

[1] TRUE

2020-05-07